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Dreux KM, Tschumper GS. Examination of the structures, energetics, and vibrational frequencies of small sulfur‐containing prototypical dimers, (H
2
S)
2
and H
2
O/H
2
S. J Comput Chem 2018; 40:229-236. [DOI: 10.1002/jcc.25578] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Katelyn M. Dreux
- Department of Chemistry and Biochemistry University of Mississippi University Mississippi, 38677‐1848
| | - Gregory S. Tschumper
- Department of Chemistry and Biochemistry University of Mississippi University Mississippi, 38677‐1848
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Abstract
Bio-inspired synthetic backbones leading to foldamers can provide effective biopolymer mimics with new and improved properties in a physiological environment, and in turn could serve as useful tools to study biology and lead to practical applications in the areas of diagnostics or therapeutics. Remarkable progress has been accomplished over the past 20 years with the discovery of many potent bioactive foldamers originating from diverse backbones and targeting a whole spectrum of bio(macro)molecules such as membranes, protein surfaces, and nucleic acids. These current achievements, future opportunities, and key challenges that remain are discussed in this article.
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3
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Rakers C, Bermudez M, Keller BG, Mortier J, Wolber G. Computational close up on protein-protein interactions: how to unravel the invisible using molecular dynamics simulations? WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2015. [DOI: 10.1002/wcms.1222] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Christin Rakers
- Institute of Pharmacy; Freie Universität Berlin; Berlin Germany
| | - Marcel Bermudez
- Institute of Pharmacy; Freie Universität Berlin; Berlin Germany
| | - Bettina G. Keller
- Institute for Chemistry and Biochemistry; Freie Universität Berlin; Berlin Germany
| | - Jérémie Mortier
- Institute of Pharmacy; Freie Universität Berlin; Berlin Germany
| | - Gerhard Wolber
- Institute of Pharmacy; Freie Universität Berlin; Berlin Germany
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4
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Mortier J, Nyakatura EK, Reimann O, Huhmann S, Daldrop JO, Baldauf C, Wolber G, Miettinen MS, Koksch B. Coiled-coils in phage display screening: insight into exceptional selectivity provided by molecular dynamics. J Chem Inf Model 2015; 55:495-500. [PMID: 25648076 DOI: 10.1021/ci500689c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Involved in numerous key biological functions, protein helix-helix interactions follow a well-defined intermolecular recognition pattern. The characteristic structure of the α-helical coiled-coil allows for the specific randomization of clearly defined interaction partners within heteromeric systems. In this work, a rationally designed heterodimeric coiled-coil was used to investigate potential factors influencing the sequence selectivity in interhelical interactions.
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Affiliation(s)
- Jérémie Mortier
- †Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Elisabeth K Nyakatura
- †Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Oliver Reimann
- †Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Susanne Huhmann
- †Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Jan O Daldrop
- ‡Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Carsten Baldauf
- Fritz Haber Institute der MPG, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gerhard Wolber
- †Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Markus S Miettinen
- ‡Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Beate Koksch
- †Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
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5
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Nyakatura EK, Mortier J, Radtke VS, Wieczorek S, Rezaei Araghi R, Baldauf C, Wolber G, Koksch B. β- and γ-Amino Acids at α-Helical Interfaces: Toward the Formation of Highly Stable Foldameric Coiled Coils. ACS Med Chem Lett 2014; 5:1300-3. [PMID: 25516788 DOI: 10.1021/ml500361c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 10/28/2014] [Indexed: 01/10/2023] Open
Abstract
Since peptides are vital for cellular and pathogenic processes, much effort has been put into the design of unnatural oligomers that mimic natural peptide structures, also referred to as foldamers. However, to enable the specific application of foldamers, a thorough characterization of their interaction profiles in native protein environments is required. We report here the application of phage display for the identification of suitable helical environments for a sequence comprising an alternating set of β- and γ-amino acids. In vitro selected sequences show that an increase in the hydrophobic surface area at the helical interface as well as the incorporation of a polar H-bond donor functionality can significantly improve interhelical interactions involving backbone-extended amino acids. Thus, our data provide insight into the principles of the rational design of foldameric inhibitors for protein-protein interactions.
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Affiliation(s)
- Elisabeth K. Nyakatura
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
| | - Jérémie Mortier
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
- Institute
of Pharmacy, Freie Universität Berlin, Königin-Luisestrasse 2 +
4, 14194 Berlin, Germany
| | - Vanessa S. Radtke
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
| | - Sebastian Wieczorek
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
| | - Raheleh Rezaei Araghi
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
| | - Carsten Baldauf
- Fritz Haber Institute, Faradayweg
4-6, 14195 Berlin, Germany
| | - Gerhard Wolber
- Institute
of Pharmacy, Freie Universität Berlin, Königin-Luisestrasse 2 +
4, 14194 Berlin, Germany
| | - Beate Koksch
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
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6
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Sharma GVM, Thodupunuri P, Sirisha K, Basha SJ, Gurava Reddy P, Sarma AVS. Design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational study. J Org Chem 2014; 79:8614-28. [PMID: 25180942 DOI: 10.1021/jo501267k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The present study is aimed at the design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational analysis (NMR, MD, and CD studies). The requisite peptides with heterogeneous backbones were prepared from β-, γ-, and δ-amino acids with carbohydrate side chains and α-amino acid, L-Ala. The α/β-peptides were prepared from (S)-β-Caa(l) (C-linked carbo-β-amino acid with D-lyxo furanoside side chain) and L-Ala with a 1:1 alternation. The α/β-peptides with "helix-turn" motif displayed a 11/9-helix nucleating a 13-atom H-bonding turn. The α/β-octapeptides showed the presence of HTH structures with bifurcated 11/15-H-bonded turn. Further, the α/β-hexapeptide with HT motif, independently on coupling with γ/α/γ/α- and δ/α/δ/α-tetrapeptides at the C-terminus provided access to the decapeptides with "hybrid HTH" motifs. The decapeptide ("α-β-α-β-α-β-γ-α-γ-α") showed a hybrid HTH with "11/9/11/9/11/16/9/12/10" H-bonding, while the decapeptide ("α-β-α-β-α-β-δ-α-δ-α") revealed the presence of a "11/9/11/9/11/17/9/13/11" helical pattern. The above peptides thus have shown compatibility between different types of helices and serendipitous bifurcated 11/16- and 11/17-turns. The present study thus provided the first opportunity for the design and study of "hybrid HTH" motifs with more than one kind of helical structures in them.
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Affiliation(s)
- Gangavaram V M Sharma
- Organic and Bimolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology , Hyderabad 500 007, India
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7
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Gord JR, Walsh PS, Fisher BF, Gellman SH, Zwier TS. Mimicking the First Turn of an α-Helix with an Unnatural Backbone: Conformation-Specific IR and UV Spectroscopy of Cyclically Constrained β/γ-Peptides. J Phys Chem B 2014; 118:8246-56. [PMID: 24694352 DOI: 10.1021/jp5015884] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Joseph R. Gord
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Patrick S. Walsh
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Brian F. Fisher
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Timothy S. Zwier
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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